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Top Forums Shell Programming and Scripting Xargs to call python executable to process multiple bam files Post 303042318 by RudiC on Saturday 21st of December 2019 09:00:10 AM
Old 12-21-2019
xargs is used to turn a stream on stdin into command line arguments / parameters. sh expects its commands on stdin. Try without xargs, like
Code:
echo "..." | sh


Or, use your .py as the xargs' command but make sure it will be interpreted by python (by defining the correct "shebang").
This User Gave Thanks to RudiC For This Post:
 

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XARGS(1L)																 XARGS(1L)

NAME
xargs - build and execute command lines from standard input SYNOPSIS
xargs [-0prtx] [-e[eof-str]] [-i[replace-str]] [-l[max-lines]] [-n max-args] [-s max-chars] [-P max-procs] [--null] [--eof[=eof-str]] [--replace[=replace-str]] [--max-lines[=max-lines]] [--interactive] [--max-chars=max-chars] [--verbose] [--exit] [--max-procs=max-procs] [--max-args=max-args] [--no-run-if-empty] [--version] [--help] [command [initial-arguments]] DESCRIPTION
This manual page documents the GNU version of xargs. xargs reads arguments from the standard input, delimited by blanks (which can be pro- tected with double or single quotes or a backslash) or newlines, and executes the command (default is /bin/echo) one or more times with any initial-arguments followed by arguments read from standard input. Blank lines on the standard input are ignored. xargs exits with the following status: 0 if it succeeds 123 if any invocation of the command exited with status 1-125 124 if the command exited with status 255 125 if the command is killed by a signal 126 if the command cannot be run 127 if the command is not found 1 if some other error occurred. OPTIONS --null, -0 Input filenames are terminated by a null character instead of by whitespace, and the quotes and backslash are not special (every character is taken literally). Disables the end of file string, which is treated like any other argument. Useful when arguments might contain white space, quote marks, or backslashes. The GNU find -print0 option produces input suitable for this mode. --eof[=eof-str], -e[eof-str] Set the end of file string to eof-str. If the end of file string occurs as a line of input, the rest of the input is ignored. If eof-str is omitted, there is no end of file string. If this option is not given, the end of file string defaults to "_". --help Print a summary of the options to xargs and exit. --replace[=replace-str], -i[replace-str] Replace occurences of replace-str in the initial arguments with names read from standard input. Also, unquoted blanks do not termi- nate arguments. If replace-str is omitted, it defaults to "{}" (like for `find -exec'). Implies -x and -l 1. --max-lines[=max-lines], -l[max-lines] Use at most max-lines nonblank input lines per command line; max-lines defaults to 1 if omitted. Trailing blanks cause an input line to be logically continued on the next input line. Implies -x. --max-args=max-args, -n max-args Use at most max-args arguments per command line. Fewer than max-args arguments will be used if the size (see the -s option) is exceeded, unless the -x option is given, in which case xargs will exit. --interactive, -p Prompt the user about whether to run each command line and read a line from the terminal. Only run the command line if the response starts with `y' or `Y'. Implies -t. --no-run-if-empty, -r If the standard input does not contain any nonblanks, do not run the command. Normally, the command is run once even if there is no input. --max-chars=max-chars, -s max-chars Use at most max-chars characters per command line, including the command and initial arguments and the terminating nulls at the ends of the argument strings. The default is as large as possible, up to 20k characters. --verbose, -t Print the command line on the standard error output before executing it. --version Print the version number of xargs and exit. --exit, -x Exit if the size (see the -s option) is exceeded. --max-procs=max-procs, -P max-procs Run up to max-procs processes at a time; the default is 1. If max-procs is 0, xargs will run as many processes as possible at a time. Use the -n option with -P; otherwise chances are that only one exec will be done. SEE ALSO
find(1L), locate(1L), locatedb(5L), updatedb(1) Finding Files (on-line in Info, or printed) XARGS(1L)
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